Variant report

Variant	rs3771129
Chromosome Location	chr2:10549436-10549437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:41)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:41 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10544615..10547096-chr2:10548655..10551250,3	K562	blood:
2	chr2:10548741..10551044-chr2:10552688..10554394,2	K562	blood:
3	chr2:10261171..10265935-chr2:10544190..10551018,10	K562	blood:
4	chr2:10328150..10328991-chr2:10548904..10549863,5	MCF-7	breast:
5	chr2:10410359..10411311-chr2:10549026..10549739,3	MCF-7	breast:
6	chr2:10440924..10446095-chr2:10544022..10551736,19	MCF-7	breast:
7	chr2:10495772..10497357-chr2:10549432..10551731,2	K562	blood:
8	chr2:10397551..10400374-chr2:10549393..10550991,2	MCF-7	breast:
9	chr2:10418216..10420909-chr2:10547555..10550904,3	K562	blood:
10	chr2:10472884..10475562-chr2:10547169..10549759,2	K562	blood:
11	chr2:10272011..10278010-chr2:10546327..10552012,10	K562	blood:
12	chr2:10445047..10447239-chr2:10547484..10549906,2	MCF-7	breast:
13	chr2:10416484..10418101-chr2:10547563..10549707,2	MCF-7	breast:
14	chr2:10266037..10268714-chr2:10547903..10550604,2	K562	blood:
15	chr2:10480270..10481880-chr2:10548259..10550783,2	MCF-7	breast:
16	chr2:10461532..10462376-chr2:10549061..10549873,2	MCF-7	breast:
17	chr2:10423718..10426925-chr2:10546888..10550753,3	MCF-7	breast:
18	chr2:10265098..10266000-chr2:10549288..10549837,2	MCF-7	breast:
19	chr2:10548229..10551901-chr2:10552572..10557970,6	K562	blood:
20	chr2:10531886..10534694-chr2:10548127..10550273,2	K562	blood:
21	chr2:10544615..10546165-chr2:10548581..10550648,2	K562	blood:
22	chr2:10379794..10381312-chr2:10548728..10550420,2	K562	blood:
23	chr2:10328455..10329154-chr2:10549215..10549757,2	K562	blood:
24	chr2:10410367..10411323-chr2:10548606..10549914,5	K562	blood:
25	chr2:10537541..10541103-chr2:10547321..10550436,3	MCF-7	breast:
26	chr2:10436642..10438745-chr2:10547775..10550649,2	K562	blood:
27	chr2:10442266..10443520-chr2:10548955..10549705,3	MCF-7	breast:
28	chr2:10543950..10547023-chr2:10547884..10550475,4	MCF-7	breast:
29	chr2:10535204..10537517-chr2:10547562..10550495,2	MCF-7	breast:
30	chr2:10547842..10550365-chr2:10556156..10557846,2	K562	blood:
31	chr2:10266037..10269086-chr2:10547903..10550826,4	K562	blood:
32	chr2:10460038..10463230-chr2:10546392..10550535,3	MCF-7	breast:
33	chr2:10270635..10275854-chr2:10544682..10552679,11	K562	blood:
34	chr2:10440762..10444214-chr2:10546694..10551810,5	K562	blood:
35	chr2:10212443..10213176-chr2:10548994..10549507,2	K562	blood:
36	chr2:10409982..10410924-chr2:10548925..10549650,2	MCF-7	breast:
37	chr15:93631076..93631748-chr2:10548940..10549868,2	MCF-7	breast:
38	chr2:10259324..10265273-chr2:10547206..10552383,9	K562	blood:
39	chr2:10548913..10551031-chr2:10587775..10589671,2	K562	blood:
40	chr2:10328070..10328961-chr2:10549008..10550652,5	MCF-7	breast:
41	chr2:10546710..10550413-chr2:10585616..10590159,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272524	Chromatin interaction
ENSG00000264030	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000115756	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12467741	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12472775	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3755263	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3755264	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3771128	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3771134	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771138	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771141	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771147	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62130186	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62130189	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62130190	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs876616	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10533000-10551800	Weak transcription	Ovary	ovary
2	chr2:10541200-10550800	Enhancers	Fetal Muscle Leg	muscle
3	chr2:10544200-10549600	Enhancers	Left Ventricle	heart
4	chr2:10544200-10549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:10544400-10549800	Enhancers	Right Ventricle	heart
6	chr2:10544800-10549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:10544800-10549600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:10544800-10549800	Enhancers	Lung	lung
9	chr2:10545200-10549800	Enhancers	Pancreas	Pancrea
10	chr2:10545400-10549600	Enhancers	Spleen	Spleen
11	chr2:10545400-10551800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:10545600-10549600	Enhancers	NH-A	brain
13	chr2:10545600-10549800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:10545800-10549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:10545800-10549800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:10545800-10550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:10546200-10549800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:10546200-10550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:10546400-10551400	Enhancers	Fetal Thymus	thymus
20	chr2:10546600-10549800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:10546600-10550600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:10546800-10549600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:10546800-10551400	Genic enhancers	Fetal Intestine Small	intestine
24	chr2:10547000-10549800	Enhancers	Adipose Nuclei	Adipose
25	chr2:10547000-10549800	Enhancers	Colon Smooth Muscle	Colon
26	chr2:10547000-10550200	Enhancers	Small Intestine	intestine
27	chr2:10547000-10551600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:10547200-10549600	Enhancers	Gastric	stomach
29	chr2:10547200-10551600	Enhancers	HSMM	muscle
30	chr2:10547400-10549600	Weak transcription	Fetal Brain Female	brain
31	chr2:10547400-10551200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:10547400-10551400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:10547600-10550800	Enhancers	Fetal Intestine Large	intestine
34	chr2:10547600-10551000	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:10547600-10551600	Enhancers	Fetal Lung	lung
36	chr2:10547800-10549800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr2:10547800-10551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:10548000-10549600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:10548000-10549600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:10548000-10549600	Enhancers	Brain Angular Gyrus	brain
41	chr2:10548000-10549800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:10548000-10549800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr2:10548000-10549800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:10548200-10549800	Flanking Active TSS	GM12878-XiMat	blood
45	chr2:10548200-10551000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr2:10548200-10551000	Enhancers	Placenta	Placenta
47	chr2:10548400-10549600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:10548400-10550000	Enhancers	Fetal Kidney	kidney
49	chr2:10548400-10550200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:10548400-10550200	Weak transcription	HSMMtube	muscle

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